You have now conducted a molecular dynamics simulation of a protein-ligand complex with GROMACS. This tutorial should not be viewed as comprehensive. There are many more types of simulations that one can conduct with GROMACS (free energy calculations, non-equilibrium MD, and normal modes analysis, just to name a few). You should also review the literature and the GROMACS manual for adjustments to the .mdp files provided here for efficiency and accuracy purposes.

If you have suggestions for improving this tutorial, if you notice a mistake, or if anything is otherwise unclear, please feel free to email me. Please note: this is not an invitation to email me for GROMACS problems. I do not advertise myself as a private tutor or personal help service. That's what the GROMACS User Forum is for. I may help you there, but only in the context of providing service to the community as a whole, not just the end user.

Happy simulating!